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Kasia Kedzierska
I am a PhD student at the University of Oxford. As a computational biologist, I use Data Science and Machine Learning to answer biological questions. Specifically, I study cancer of the uterus and chromatin organisation in disease progression. My work includes data exploration, data visualisation and communicating results to non-technical audience. For example, I take advantage of feature selection and dimensionality reduction methods, generate hypothesis with unsupervised learning and test them with in silico and in vitro experiments. I model complex biological processes with a repertoire of ML models - from Linear Models to Deep Learning.
Last summer, I joined Computational Biology Department at Novo Nordisk Research Centre in Oxford as an intern, where I worked with NLP methods and knowledge graphs. Currently, I am looking into adapting my experience from the internship to build models investigating cancer evolution.
Selected Work Experience
Intern @ Novo Nordisk Research Centre Oxford, Oxford, United Kingdom
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2021
- I used NLP based methods to screen biomedical articles and identify potential therapeutic targets. I built R Shiny App to allow colleagues within the company to investigate results from our pipeline.
DPhil Candidate @ Wellcome Centre for Human Genetics, Big Data Institute, University of Oxford, UK
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present - 2018
- In my PhD project Functional and evolutionary characterisation of chromatin organisation in endometrial cancer I am looking at how chromatin organisation influences disease progression in cancer of the uterus.
- Currently I’m working on building and refining ML models of cancer evolution.
Education
DPhil. Candidate, Genomic Medicine and Statistics @ Nuffield Department of Medicine, Brasenose College, University of Oxford, UK
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present - 2018
- PhD fully funded by Wellcome Trust Four-year PhD Studentships in Science
M. Sc. Eng., Biotechnology @ Warsaw University of Technology, Warsaw, Poland
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2018 - 2015
- Master thesis: - Analysis of the mutational burden across gene sets in cancer awarded the title of The Best Master Thesis in Bioinformatics defended in 2018.
Selected Awards and Honors
Senior Hulme Scholarship
Brasenose College, University of Oxford
Oxford, UK
present - 2021
- Senior Hulme Scholarship is awarded by Brasenose College, University of Oxford to DPhil students whose academic performance is deemed to be exceptional.
Graduate Prize in the ‘Outstanding work outside degree’ category
Nuffield Department of Medicine, University of Oxford
Oxford, UK
2022 - 2021
- Each year Nuffield Department of Medicine, based on nominations, awards selected PhD students based on their performance within and outside of their degree.
Attended Workshops, Summer Schools
Machine Learning Summer School
Imperial College London, University College London
London, United Kingdom
2019
Selected Publications
Full list of publication is available through my Google Scholar profile scholar.google.com/citations?user=Yv6poTwAAAAJ.
Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift @ BMC Genomics
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2021
M. Migdal, E. Tralle, K. A. Nahia, L. Bugajski, K. Z. Kedzierska, F. Garbicz, K. Piwocka, C. L. Winata, M. Pawlak
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability @ Clinical Epigenetics
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2020
H. Russell, K. Kedzierska, D. D. Buchanan, R. Thomas, E. Tham, M. Mints, A. Keränen, G. G. Giles, M. C. Southey, R. L. Milne, I. Tomlinson, D. Church, A. B. Spurdle, T. A. O’Mara and A. Lewis
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development @ Genome Research
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2019
M. Pawlak, K. Z. Kedzierska, M. Migdal, K. A. Nahia, J. A. Ramilowski, L. Bugajski, K. Hashimoto, A. Marconi, K. Piwocka, P. Carninci and C. L. Winata
SONiCS: PCR stutter noise correction in genome-scale microsatellites @ Bioinformatics
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2018
K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan, L. Kistler
Selected Conference Presentations
Poster presentation: Systematic characterisation of chromatin modifiers in endometrial cancer @ European Association for Cancer Research 2022 Congress
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2022
Invited talk: Analysis of the mutational burden across gene sets in cancer @ Polish Bioinformatics Society Symposium
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2019
Poster: Differential mutation analysis across gene sets in cancers @ Biology of Genomes 2018
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2018
Teaching Experience
Unsupervised learning @ NGSchool2022: Machine Learning in Computational Biology
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2022
- I co-led, with Kaspar Märtens, lecture and tutorial sessions on unsupervised learning and its use cases in computational biology. All materials are availble at github.com/kzkedzierska/ngs22_unsupervised.
Data visualization in bioinformatics - hackathon mentor @ Online hackathon NGSprint
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2021
- I led the hackathon in data viusalisation with emphasis on computational biology. Teaching materials are available at github.com/kzkedzierska/NGSprint_data_viz.
Online tutorials: Python for Data Science and Introduction to Python @ NGSeminars
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2020
- I led two Python tutorials: Introduction to Python kasia.codes/talk/intro_to_python/ and Python for Data Science kasia.codes/talk/py4ds/.
Introduction to R @ Wellcome Centre for Human Genetics
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2019
- 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
- Materials available on github/kzkedziersa/r_intro
Introduction to Managing Code with Git @ Wellcome Centre for Human Genetics
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2020 - 2019
- I led a 2-hour introduction to working with Git. Materials, including slides and exercises are available at kasia.codes/talk/into_to_git/.
Selected Grants
Visegrad Grant to organize NGSchool2022 @ Visegrad Fund
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2022 - 2020
- 32,190 EUR awarded towards organising affordable training and conference focusing on ML application in Computational Biology. During this project I managed an international team of volunteers and led the organisation of summer school, conference, online seminars and hackathon.
Non-profit Work
President @ NGSchool Society
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present - 2018
- The goal of the Society is to promote and support science, with emphasis on computational biology.
- President since 2019; Vice President 2018 - 2019, Founder